ENT MERFISH Report

1.1 Overview

1.1.1 Sample Information

A brief sample information is generated from the submission table for the following analysis.

Sample Index and Basic Information
Expt Sample Index Case_Number Sex Age HPV Sample_Region Genotype Group Region DataPath Clinic.comment
5 2 TT29258 TT29258 3 M 47 Positive Right tongue cancer TT Tumor region_0 Y:_Imaging_data_2\202412061704_20241206ENT2925859ImmunOncoh500x03_VMSC00101 right tongue cancer, involving the right hemitongue and base of tongue, cT4N2bM0
6 2 NT29259 NT29259 3 M 47 Positive Right tongue cancer NT Normal region_1 Y:_Imaging_data_2\202412061704_20241206ENT2925859ImmunOncoh500x03_VMSC00101 right tongue cancer, involving the right hemitongue and base of tongue, cT4N2bM0

1.1.2 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Generally, log10 transcript count > 4.0 in most area can be considered as a good quality standard for human tissue.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

1.1.2.1 TT29258(Tumor)

1.1.2.2 NT29259(Normal)

2. Data Processing & Analysis

2.1 Cell Segmentation & Filtering

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 2000], and the gene count per cell > 25.

After that, we successfully obtained high-quality and accurate cell and gene data. We are now ready to perform statistical analysis.

For analysis platform, all of the analysis and visualization are performed using Scanpy, a commonly used Python package toolkit for analyzing single-cell gene expression data.

2.1.1 Transcript Count Violin

The transcript level is a basic aspect of data quality control. After filtering, we have ensured that the minimum transcript count per cell > 25.

Transcript Count Violin After Filtering

Transcript Count Violin After Filtering

2.2 Dimension Reduction

We conducted Leiden UMAP clustering, a non-linear, manifold-aware dimension reduction algorithm, on our dataset to subset the cells into clusters. The following annotations are based on the umap clustering.

Umap and subclusters on all batch data

Umap and subclusters on all batch data

Umap colored by groups

Umap colored by groups

3.Cell Annotation

To annotate individual cell types, we found the marker genes from database CellMarker.

It is good to note that, so far what we have is a preliminary annotation, and we can potentially achieve further resolution on some cell types. For instance, T cells can be subdivided into regulatory T cells, helper T cells, natural killer T cells, and so on. However, the current sample size is insufficient for these detailed classifications. Once we have enough samples, further annotation should be feasible.

3.1 Markers for type annotation

Cell markers dot plot, colored by expression

Cell markers dot plot, colored by expression

3.2 Cell Type Umap

Umap colored by cell type annotation

Umap colored by cell type annotation

Umap colored by cell type annotation, split by group

Umap colored by cell type annotation, split by group

3.3 Cell Type Spatial Map

With the annotations, we can map cell types back to their physical positions and create a spatial map for each sample.

Cell type spatial map, Tumor tissue

Cell type spatial map, Tumor tissue

Cell type spatial map, Normal tissue

Cell type spatial map, Normal tissue

3.3 Higher Resolution Cell Subtypes

3.3.1 Epithelial cell

Epithelial cells Umap

Epithelial cells Umap

Epithelial cells subtype markers umap

Epithelial cells subtype markers umap

3.3.2 Fibroblast cell

Fibroblast Umap

Fibroblast Umap

Fibroblast subtype markers umap

Fibroblast subtype markers umap

Fibroblast subtype spatial map on Tumor Tissue

Fibroblast subtype spatial map on Tumor Tissue

Fibroblast subtype spatial map on Tumor Tissue, Zoom-in

Fibroblast subtype spatial map on Tumor Tissue, Zoom-in

Fibroblast subtype spatial map on Normal Tissue

Fibroblast subtype spatial map on Normal Tissue

Fibroblast subtype spatial map on Normal Tissue, Zoom-in

Fibroblast subtype spatial map on Normal Tissue, Zoom-in

3.4 Cell Type Qualification Analysis

Cell Type Count Table
Cell Type Normal Tumor Total
B cell 4 4508 4512
Dendritic cell 2 370 372
Endothelial cell 2455 2371 4826
Epithelial cell 9 5556 5565
Fibroblast 8767 10207 18974
Lymphatic Endothelial cell 165 274 439
Macrophage 657 1456 2113
Mast cell 75 139 214
T cell 156 902 1058
Total 12290 25783 38073
Cell Count Barplot Comparision

Cell Count Barplot Comparision

4. Gene differentiation (Tumor v.s. Normal)

Here, we use Wilcoxon rank-sum test to compute gene differential expression (DE). P value are adjusted using Benjamini–Hochberg procedure. The statistical significance was cut-off by log2(Fold Change) > 1 or log2(Fold Change) < -1 and adjusted p_value < 0.05.

The result are visualized via Volcano plot: a type of scatterplot that shows statistical significance (P value) versus magnitude of change (fold change).

The comparison is between Tumor and Normal samples. A positive fold change means higher expression in the tumor group.

4.1 all

X p_val avg_log2FC pct.1 pct.2 p_val_adj
LYZ 0e+00 8.412063 0.497 0.009 0.0000000
SOCS3 0e+00 -1.511249 0.298 0.625 0.0000000
XBP1 0e+00 4.064851 0.377 0.056 0.0000000
MYC 0e+00 -1.653150 0.222 0.502 0.0000000
MZB1 0e+00 7.308786 0.207 0.004 0.0000000
POU2AF1 0e+00 6.309540 0.180 0.006 0.0000000
DES 0e+00 -1.627221 0.097 0.260 0.0000000
PDK4 0e+00 -2.970076 0.074 0.235 0.0000000
NRP1 0e+00 -1.789845 0.079 0.229 0.0000000
SOX9 0e+00 2.925345 0.174 0.034 0.0000000
DERL3 0e+00 5.473586 0.143 0.007 0.0000000
FCRL5 0e+00 6.986633 0.113 0.001 0.0000000
CD79A 0e+00 4.998809 0.106 0.005 0.0000000
NCAM1 0e+00 -1.755698 0.056 0.163 0.0000000
IRF4 0e+00 4.498927 0.103 0.008 0.0000000
THBD 0e+00 -1.397073 0.084 0.204 0.0000000
FN1 0e+00 -1.328376 0.136 0.269 0.0000000
EPHB3 0e+00 3.699516 0.105 0.011 0.0000000
ICAM3 0e+00 3.023489 0.115 0.017 0.0000000
PIK3CG 0e+00 3.539874 0.111 0.016 0.0000000
ITGA5 0e+00 -1.540971 0.066 0.169 0.0000000
LRP5 0e+00 1.657768 0.238 0.105 0.0000000
SH2D1B 0e+00 -3.512037 0.008 0.061 0.0000000
CAV1 0e+00 -1.944956 0.036 0.117 0.0000000
COL5A1 0e+00 -1.118630 0.162 0.287 0.0000000
VEGFA 0e+00 -1.588182 0.291 0.399 0.0000000
TNFRSF13C 0e+00 3.731769 0.085 0.010 0.0000000
ITGB1 0e+00 -1.283718 0.076 0.167 0.0000000
CD27 0e+00 4.118161 0.067 0.004 0.0000000
VWF 0e+00 -1.194784 0.093 0.188 0.0000000
CLDN5 0e+00 -1.269210 0.067 0.151 0.0000000
AKT3 0e+00 -1.624086 0.035 0.099 0.0000000
SOX2 0e+00 2.269660 0.084 0.016 0.0000000
TGFBR3 0e+00 -1.410462 0.056 0.130 0.0000000
TEAD1 0e+00 -1.124805 0.113 0.206 0.0000000
CDH5 0e+00 -1.591218 0.042 0.109 0.0000000
IL6 0e+00 -2.040224 0.026 0.081 0.0000000
CXCR4 0e+00 2.169945 0.098 0.026 0.0000000
NEDD4 0e+00 -1.851803 0.026 0.079 0.0000000
CDH1 0e+00 2.931915 0.058 0.007 0.0000000
PKM 0e+00 -1.000589 0.313 0.402 0.0000000
CCL28 0e+00 3.839878 0.049 0.004 0.0000000
GATA3 0e+00 2.633034 0.059 0.009 0.0000000
MMRN2 0e+00 -1.202717 0.067 0.136 0.0000000
IFNGR1 0e+00 -2.352728 0.009 0.043 0.0000000
AMOTL2 0e+00 -1.032383 0.092 0.168 0.0000000
PDGFRA 0e+00 -1.225705 0.064 0.129 0.0000000
PREX2 0e+00 -1.705083 0.021 0.065 0.0000000
TEAD4 0e+00 -1.348546 0.036 0.087 0.0000000
ZEB1 0e+00 -1.442518 0.031 0.079 0.0000000
CSF3 0e+00 -1.717423 0.020 0.061 0.0000000
ICAM1 0e+00 -1.029325 0.113 0.187 0.0000000
ERBB3 0e+00 1.996856 0.058 0.013 0.0000000
JAK1 0e+00 -1.017868 0.068 0.127 0.0000000
CCL2 0e+00 -2.010041 0.016 0.051 0.0000000
LDHA 0e+00 -1.485012 0.026 0.067 0.0000000
ERBB2 0e+00 1.056178 0.157 0.088 0.0000000
CLEC14A 0e+00 -1.126421 0.050 0.100 0.0000000
KDR 0e+00 -1.188290 0.044 0.091 0.0000000
NFE2L2 0e+00 -1.159824 0.042 0.089 0.0000000
TNFRSF18 0e+00 2.834298 0.037 0.006 0.0000000
PDK1 0e+00 1.359399 0.084 0.037 0.0000000
TNFRSF13B 0e+00 3.122099 0.031 0.004 0.0000000
EPHA4 0e+00 -1.759985 0.012 0.038 0.0000000
DNMT3A 0e+00 -1.276937 0.030 0.066 0.0000000
TP63 0e+00 -1.420061 0.023 0.055 0.0000000
CDK2 0e+00 -1.036278 0.047 0.087 0.0000000
APC 0e+00 -1.136881 0.029 0.062 0.0000000
TNFRSF17 0e+00 2.136179 0.035 0.008 0.0000000
WNT3A 0e+00 -1.343337 0.023 0.052 0.0000000
MCM6 0e+00 -1.251976 0.022 0.051 0.0000000
COL6A3 0e+00 -1.951578 0.007 0.026 0.0000000
ITGB2 0e+00 1.076275 0.073 0.034 0.0000000
MAFB 0e+00 -1.007535 0.047 0.085 0.0000000
PPARGC1A 0e+00 -1.565611 0.013 0.036 0.0000000
ITGA1 0e+00 -2.073867 0.006 0.022 0.0000000
MET 0e+00 -1.298848 0.018 0.043 0.0000000
ANGPT2 0e+00 -1.520383 0.011 0.031 0.0000000
SMAD2 0e+00 -1.217907 0.020 0.044 0.0000000
S100A9 0e+00 -1.030151 0.024 0.050 0.0000000
PTGS2 0e+00 -1.216101 0.025 0.051 0.0000000
TWIST1 0e+00 -1.225380 0.017 0.039 0.0000000
TEK 0e+00 -1.567924 0.009 0.026 0.0000000
SELPLG 0e+00 1.817132 0.028 0.008 0.0000000
TGFBR1 0e+00 -1.319656 0.013 0.032 0.0000000
TGFBI 0e+00 -1.072106 0.031 0.058 0.0000000
IL3RA 0e+00 -1.366550 0.014 0.033 0.0000000
CD19 0e+00 2.239572 0.018 0.004 0.0000000
FGF2 0e+00 -1.243160 0.013 0.029 0.0000000
CLCA1 0e+00 -1.341954 0.010 0.024 0.0000000
NOS3 0e+00 -1.003980 0.022 0.042 0.0000000
CXCL5 0e+00 1.853385 0.023 0.007 0.0000000
MSH3 0e+00 -1.051553 0.019 0.038 0.0000000
ATR 0e+00 -1.007653 0.020 0.039 0.0000000
CTSW 0e+00 1.367663 0.034 0.015 0.0000000
PDGFA 0e+00 -1.118203 0.015 0.031 0.0000000
HGF 0e+00 -1.483973 0.006 0.017 0.0000000
TBK1 0e+00 -1.398243 0.007 0.019 0.0000000
BLK 0e+00 1.466196 0.029 0.012 0.0000000
CCL5 0e+00 1.366203 0.023 0.010 0.0000000
CCL4 0e+00 1.889099 0.017 0.006 0.0000000
CD22 0e+00 1.195480 0.025 0.011 0.0000000
RB1 0e+00 -1.664314 0.004 0.011 0.0000000
PDCD1 0e+00 1.588784 0.016 0.005 0.0000000
PLOD2 0e+00 1.185767 0.022 0.010 0.0000000
CD3E 0e+00 1.317308 0.021 0.009 0.0000000
LGR5 0e+00 -1.064377 0.012 0.023 0.0000000
CA7 0e+00 -1.421237 0.005 0.013 0.0000000
RET 0e+00 -1.452582 0.006 0.014 0.0000000
BRCA1 0e+00 -1.152420 0.009 0.018 0.0000000
IL12A 0e+00 -1.051929 0.010 0.019 0.0000000
TRAC 0e+00 1.295637 0.015 0.007 0.0000000
CEACAM1 0e+00 1.666131 0.010 0.003 0.0000000
CD209 0e+00 -1.254727 0.008 0.015 0.0000000
SERPINA1 0e+00 1.339149 0.010 0.004 0.0000000
CCR7 0e+00 1.321011 0.019 0.010 0.0000000
CCR1 0e+00 -1.075956 0.008 0.014 0.0000001
IL2RB 0e+00 1.036558 0.019 0.011 0.0000009
MRC1 9e-07 -1.165749 0.029 0.039 0.0004541

4.2 Endothelial cell

X p_val avg_log2FC pct.1 pct.2 p_val_adj
LYZ 0.0000000 5.666966 0.330 0.011 0.0000000
MYC 0.0000000 -1.206533 0.384 0.594 0.0000000
CAV1 0.0000000 -1.423155 0.162 0.343 0.0000000
ITGB1 0.0000000 -1.494093 0.075 0.198 0.0000000
ATF3 0.0000000 -1.065250 0.138 0.242 0.0000000
EPHA4 0.0000000 -1.306204 0.062 0.141 0.0000000
IFNGR1 0.0000000 -2.555494 0.009 0.053 0.0000000
TEK 0.0000000 -1.529322 0.037 0.099 0.0000000
AKT3 0.0000000 -1.154887 0.059 0.124 0.0000000
JAK1 0.0000000 -1.021326 0.070 0.136 0.0000000
ITGA1 0.0000000 -1.801250 0.019 0.061 0.0000000
S100A9 0.0000000 -2.203529 0.011 0.046 0.0000000
FLT1 0.0000000 -1.201836 0.045 0.099 0.0000000
CCL2 0.0000000 -1.690685 0.027 0.072 0.0000000
ZEB1 0.0000000 -1.198516 0.038 0.085 0.0000000
IL6 0.0000000 -1.381026 0.064 0.118 0.0000000
FN1 0.0000000 -1.187213 0.073 0.130 0.0000000
CXCL2 0.0000000 -1.547851 0.027 0.067 0.0000000
MZB1 0.0000000 2.230800 0.023 0.004 0.0000113
MET 0.0000001 -1.205612 0.027 0.059 0.0000440
IFNAR2 0.0000002 -1.325640 0.017 0.043 0.0000832
CCND1 0.0000002 -1.106498 0.024 0.053 0.0000991
KRAS 0.0000006 -2.049308 0.005 0.022 0.0003054
TBK1 0.0000007 -2.162766 0.004 0.020 0.0003264
LDHA 0.0000013 -1.245229 0.016 0.040 0.0006415
IFNAR1 0.0000137 -3.119698 0.001 0.010 0.0068575
BRAF 0.0000181 -1.222791 0.015 0.034 0.0090734
PCNA 0.0000455 -2.704660 0.001 0.010 0.0227415
FLI1 0.0000857 -1.913247 0.004 0.015 0.0428728
POU2AF1 0.0000942 2.335630 0.013 0.003 0.0471100
SOX9 0.0004292 1.437250 0.013 0.004 0.2145890
TBX3 0.0005012 -1.137400 0.014 0.029 0.2505768
STAT1 0.0007764 -1.497260 0.005 0.015 0.3881880
MMP11 0.0015413 -1.013903 0.013 0.026 0.7706589
HGF 0.0024255 -1.151406 0.008 0.018 1.0000000
KLRB1 0.0039506 -1.112044 0.008 0.018 1.0000000
TGFBI 0.0044445 -1.065250 0.010 0.020 1.0000000
LAMC2 0.0076573 -1.030693 0.011 0.020 1.0000000
SELPLG 0.0080948 1.291235 0.011 0.004 1.0000000
CCR4 0.0081196 1.220152 0.011 0.004 1.0000000
CXCL10 0.0089863 -1.271701 0.005 0.013 1.0000000
MMP2 0.0277947 1.050227 0.011 0.005 1.0000000

4.3 Fibroblast

X p_val avg_log2FC pct.1 pct.2 p_val_adj
LYZ 0.0e+00 5.983536 0.293 0.008 0.0000000
SOCS3 0.0e+00 -1.289538 0.363 0.602 0.0000000
PDK4 0.0e+00 -2.623900 0.113 0.301 0.0000000
MYC 0.0e+00 -1.000314 0.318 0.497 0.0000000
VEGFA 0.0e+00 -1.342015 0.392 0.519 0.0000000
SH2D1B 0.0e+00 -3.568615 0.010 0.084 0.0000000
PKM 0.0e+00 -1.047948 0.299 0.436 0.0000000
NRP1 0.0e+00 -1.183704 0.123 0.232 0.0000000
IL6R 0.0e+00 -1.133144 0.120 0.225 0.0000000
NCAM1 0.0e+00 -1.097307 0.113 0.216 0.0000000
S100A9 0.0e+00 -3.437584 0.005 0.044 0.0000000
RORC 0.0e+00 -1.350834 0.068 0.141 0.0000000
MZB1 0.0e+00 3.672614 0.039 0.004 0.0000000
TGFBR3 0.0e+00 -1.174701 0.073 0.143 0.0000000
CSF3 0.0e+00 -1.707871 0.018 0.060 0.0000000
DNMT3A 0.0e+00 -1.282347 0.034 0.076 0.0000000
ZEB1 0.0e+00 -1.190035 0.038 0.081 0.0000000
NEDD4 0.0e+00 -1.212746 0.048 0.092 0.0000000
IFNGR1 0.0e+00 -1.766892 0.013 0.040 0.0000000
MAFB 0.0e+00 -1.163550 0.043 0.083 0.0000000
COL6A3 0.0e+00 -1.822233 0.010 0.034 0.0000000
MCM6 0.0e+00 -1.171352 0.028 0.060 0.0000000
APC 0.0e+00 -1.051329 0.032 0.064 0.0000000
CDK2 0.0e+00 -1.022130 0.042 0.077 0.0000000
TP63 0.0e+00 -1.052019 0.039 0.072 0.0000000
PPARGC1A 0.0e+00 -1.277059 0.020 0.047 0.0000000
CAV1 0.0e+00 -1.057516 0.032 0.063 0.0000000
IL6 0.0e+00 -1.145801 0.044 0.078 0.0000000
WNT5A 0.0e+00 -1.332785 0.015 0.037 0.0000000
PREX2 0.0e+00 -1.092871 0.025 0.050 0.0000000
RET 0.0e+00 -2.202916 0.004 0.017 0.0000000
CD79A 0.0e+00 2.409413 0.015 0.003 0.0000000
MSH6 0.0e+00 -1.162820 0.020 0.041 0.0000000
MSH3 0.0e+00 -1.142783 0.019 0.041 0.0000000
MUC4 0.0e+00 -1.361273 0.014 0.033 0.0000000
ATR 0.0e+00 -1.058123 0.020 0.040 0.0000000
POU2AF1 0.0e+00 1.669339 0.020 0.007 0.0000000
SERPINE1 0.0e+00 1.011993 0.095 0.064 0.0000000
TBK1 0.0e+00 -1.419341 0.007 0.019 0.0000000
CCL2 0.0e+00 -1.095452 0.023 0.040 0.0000000
ANGPT2 0.0e+00 -1.151806 0.013 0.027 0.0000000
CIITA 0.0e+00 1.145058 0.026 0.013 0.0000001
CA7 0.0e+00 -1.414660 0.007 0.016 0.0000001
DERL3 0.0e+00 1.330369 0.018 0.008 0.0000011
RB1 0.0e+00 -1.600833 0.004 0.011 0.0000020
BRCA1 0.0e+00 -1.219404 0.008 0.017 0.0000058
C1QC 0.0e+00 1.202829 0.012 0.005 0.0000202
EPHA4 1.0e-07 -1.267498 0.006 0.013 0.0000385
STAT4 2.0e-07 -1.085652 0.009 0.018 0.0000864
IL23A 7.0e-07 -1.157247 0.008 0.016 0.0003647
KITLG 2.9e-06 -1.283534 0.004 0.010 0.0014402

4.4 Lymphatic Endothelial cell

X p_val avg_log2FC pct.1 pct.2 p_val_adj
LYZ 0.0000000 6.210805 0.248 0.000 0.0000000
MYC 0.0000000 -1.199859 0.394 0.594 0.0000093
PECAM1 0.0000013 -1.731710 0.157 0.333 0.0006748
TGFBR3 0.0002343 -1.355147 0.124 0.255 0.1171387
TEAD1 0.0005706 -1.172282 0.175 0.303 0.2853081
TBX3 0.0009160 -2.731710 0.007 0.061 0.4580133
COL5A1 0.0012811 -1.032369 0.186 0.309 0.6405427
PDCD1LG2 0.0013491 -2.901635 0.004 0.048 0.6745327
S100A9 0.0013491 -2.901635 0.004 0.048 0.6745327
TAPBP 0.0024591 -1.664596 0.036 0.109 1.0000000
CDKN1B 0.0025126 -1.539065 0.040 0.115 1.0000000
NCAM1 0.0025287 -1.333746 0.172 0.279 1.0000000
TCF7L2 0.0026774 -1.053638 0.113 0.218 1.0000000
HIF1A 0.0028888 -1.255272 0.102 0.200 1.0000000
ITGB1 0.0037477 -1.316672 0.077 0.164 1.0000000
KIT 0.0038210 -3.316672 0.000 0.030 1.0000000
IL6R 0.0043802 -1.568211 0.040 0.109 1.0000000
BCL2 0.0049035 -1.316672 0.044 0.115 1.0000000
VSIR 0.0050755 -1.497245 0.033 0.097 1.0000000
CDK6 0.0063539 -1.194682 0.120 0.212 1.0000000
MSH3 0.0066703 -2.191142 0.011 0.055 1.0000000
MAML1 0.0081686 -1.021216 0.164 0.261 1.0000000
NFE2L2 0.0088845 -1.246283 0.044 0.109 1.0000000
AKT3 0.0089459 -1.657709 0.033 0.091 1.0000000
LGALS9 0.0090755 2.268290 0.066 0.012 1.0000000
MET 0.0094197 -1.624795 0.022 0.073 1.0000000
CDK2 0.0129496 -1.348381 0.051 0.115 1.0000000
ZEB1 0.0138677 -1.316672 0.047 0.109 1.0000000
SMARCA4 0.0174203 -1.272278 0.036 0.091 1.0000000
TGFBI 0.0177206 -1.344687 0.058 0.121 1.0000000
IFNGR2 0.0179199 -1.132248 0.077 0.145 1.0000000
IFNGR1 0.0199695 -2.539065 0.004 0.030 1.0000000
XBP1 0.0209024 1.753717 0.077 0.024 1.0000000
LAG3 0.0254584 -2.731710 0.000 0.018 1.0000000
MYH11 0.0254584 -2.731710 0.000 0.018 1.0000000
SNAI1 0.0270414 2.727722 0.029 0.000 1.0000000
INSR 0.0306312 -1.025441 0.102 0.170 1.0000000
GPX3 0.0334207 -1.011818 0.077 0.139 1.0000000
RGMB 0.0355655 -1.539065 0.022 0.061 1.0000000
BRAF 0.0364306 -1.383787 0.022 0.061 1.0000000
ACTA2 0.0369911 -1.579707 0.026 0.067 1.0000000
BRCA1 0.0494136 -2.053638 0.004 0.024 1.0000000
CTSW 0.0494136 -2.053638 0.004 0.024 1.0000000

4.5 Macrophage

X p_val avg_log2FC pct.1 pct.2 p_val_adj
LYZ 0.0000000 4.628310 0.326 0.026 0.0000000
MRC1 0.0000000 -1.404869 0.400 0.609 0.0000000
MYC 0.0000000 -1.756063 0.141 0.318 0.0000000
CCR1 0.0000000 -1.839095 0.053 0.163 0.0000000
CCL2 0.0000000 -2.413017 0.038 0.125 0.0000000
MZB1 0.0000000 5.087171 0.082 0.003 0.0000000
S100A9 0.0000000 -2.148045 0.037 0.117 0.0000000
TGFBI 0.0000000 -1.091663 0.163 0.291 0.0000000
SOCS3 0.0000000 -1.037559 0.229 0.355 0.0000000
CD209 0.0000000 -1.559770 0.065 0.145 0.0000005
CCL4 0.0000000 1.582996 0.120 0.038 0.0000014
CCL8 0.0000000 -2.007182 0.027 0.084 0.0000015
ITGAX 0.0000000 1.402648 0.188 0.091 0.0000039
NRP1 0.0000000 -1.189865 0.082 0.161 0.0000148
IFNGR1 0.0000001 -2.354496 0.008 0.043 0.0000399
TGFBR1 0.0000003 -1.852589 0.018 0.059 0.0001479
POU2AF1 0.0000012 3.161810 0.048 0.006 0.0005825
APC 0.0000028 -1.235508 0.030 0.075 0.0014060
CAV1 0.0000216 -2.389053 0.007 0.030 0.0107953
IL12RB2 0.0000224 -2.428153 0.004 0.024 0.0111907
EZH2 0.0000237 -2.226048 0.005 0.026 0.0118532
CCL3 0.0000284 1.006677 0.124 0.064 0.0141808
VWF 0.0000454 -1.352404 0.026 0.062 0.0226796
CD27 0.0000505 2.790554 0.028 0.002 0.0252307
CD79A 0.0000845 2.366528 0.041 0.009 0.0422450
MMRN1 0.0000950 2.758846 0.030 0.003 0.0474899
LDHA 0.0001413 -1.321377 0.030 0.065 0.0706496
ELN 0.0002192 -1.848485 0.009 0.030 0.1096187
MMP9 0.0002674 3.221189 0.035 0.008 0.1336831
FCRL5 0.0003504 3.099882 0.023 0.002 0.1751811
PTK2 0.0004409 -1.072757 0.038 0.073 0.2204719
ICAM3 0.0005493 1.368530 0.061 0.026 0.2746746
SOX9 0.0006290 1.956292 0.038 0.011 0.3145148
MSH6 0.0009251 -1.379371 0.015 0.038 0.4625567
EPHA2 0.0013001 -1.226048 0.008 0.026 0.6500278
AKT3 0.0018496 -1.188687 0.023 0.049 0.9248064
CD86 0.0026540 -1.925653 0.004 0.017 1.0000000
HGF 0.0028253 -2.022514 0.003 0.015 1.0000000
NCAM1 0.0071509 -1.495968 0.014 0.032 1.0000000
IKZF2 0.0074064 -1.041130 0.019 0.038 1.0000000
SMARCA4 0.0074633 -1.148045 0.016 0.035 1.0000000
TSC1 0.0074633 -1.148045 0.016 0.035 1.0000000
DUSP6 0.0075918 -1.083915 0.014 0.032 1.0000000
ITGA1 0.0077359 -2.148045 0.002 0.011 1.0000000
IL17A 0.0080921 -1.495968 0.007 0.020 1.0000000
MYBL2 0.0094632 1.120444 0.034 0.014 1.0000000
IL2RB 0.0112652 1.574421 0.021 0.006 1.0000000
BTLA 0.0117893 -1.247581 0.008 0.021 1.0000000
TNFRSF13B 0.0121061 1.910849 0.016 0.003 1.0000000
ATR 0.0133811 -1.148045 0.014 0.030 1.0000000
ERBB3 0.0151793 -1.800122 0.004 0.014 1.0000000
FGFR3 0.0151793 -2.041130 0.004 0.014 1.0000000
CD244 0.0194380 -1.826117 0.003 0.011 1.0000000
SPP1 0.0194553 2.289360 0.022 0.008 1.0000000
PLK1 0.0199390 -1.148045 0.011 0.024 1.0000000
CD3E 0.0240185 1.495811 0.016 0.005 1.0000000
TNFRSF13C 0.0240628 1.484223 0.030 0.014 1.0000000
PLOD2 0.0275627 1.337382 0.019 0.006 1.0000000
IL13 0.0291508 -1.469973 0.005 0.014 1.0000000
ITGA4 0.0296544 -1.065583 0.012 0.024 1.0000000
PREX2 0.0324837 1.132063 0.023 0.009 1.0000000
KLRK1 0.0406180 1.588920 0.012 0.003 1.0000000
BIRC5 0.0406657 1.514920 0.012 0.003 1.0000000
CCR8 0.0409892 -1.563083 0.003 0.011 1.0000000
CD207 0.0409892 -1.563083 0.003 0.011 1.0000000
CXCL9 0.0410708 1.099882 0.012 0.003 1.0000000
TGM2 0.0423443 -1.070043 0.012 0.024 1.0000000
CCR7 0.0458856 2.118742 0.019 0.008 1.0000000

4.6 Mast cell

X p_val avg_log2FC pct.1 pct.2 p_val_adj
KIT 0.0000000 -1.880161 0.683 0.973 0.0000000
NFKB2 0.0000000 -1.819156 0.453 0.773 0.0000000
CSF1 0.0000001 1.891667 0.719 0.413 0.0000449
JUN 0.0000001 1.832344 0.633 0.267 0.0000506
SOCS3 0.0000001 -2.165757 0.144 0.453 0.0000649
CTNNB1 0.0000008 -2.231159 0.072 0.333 0.0004220
CTSG 0.0000018 -1.251350 0.561 0.813 0.0009083
CD274 0.0000158 -2.252693 0.094 0.320 0.0079050
CD276 0.0000671 -2.764591 0.036 0.200 0.0335450
MAML1 0.0001696 -1.627088 0.158 0.373 0.0847972
CDK4 0.0001959 -3.475085 0.007 0.120 0.0979691
NRP1 0.0002628 -4.212051 0.000 0.093 0.1313754
LYZ 0.0005254 3.864765 0.173 0.013 0.2626881
ITGA4 0.0007516 -3.697477 0.000 0.080 0.3758127
MLH1 0.0010126 -2.797013 0.022 0.133 0.5063006
NFKB1 0.0012032 -2.091756 0.050 0.187 0.6015991
CDKN1A 0.0014610 -1.641095 0.158 0.333 0.7304817
NFE2L2 0.0022168 -2.890122 0.014 0.107 1.0000000
MYC 0.0025520 -2.282440 0.050 0.173 1.0000000
IL4I1 0.0031964 -2.082768 0.029 0.133 1.0000000
PTGS2 0.0037840 -1.812120 0.187 0.347 1.0000000
PKM 0.0040213 -1.021367 0.209 0.387 1.0000000
AKT3 0.0061984 -3.475085 0.000 0.053 1.0000000
EZH2 0.0061995 -3.212051 0.000 0.053 1.0000000
CD4 0.0065241 -2.082768 0.043 0.147 1.0000000
CREBBP 0.0082255 -1.277146 0.165 0.307 1.0000000
MZB1 0.0090841 3.279803 0.086 0.000 1.0000000
IFNGR2 0.0099302 -1.627088 0.094 0.213 1.0000000
BCL2L1 0.0114566 -1.420637 0.094 0.213 1.0000000
STAT3 0.0162517 -2.005600 0.036 0.120 1.0000000
IKBKB 0.0171530 -1.227157 0.108 0.227 1.0000000
TNFRSF9 0.0176298 -2.060047 0.022 0.093 1.0000000
HGF 0.0181091 -3.212051 0.000 0.040 1.0000000
MSH6 0.0181091 -3.212051 0.000 0.040 1.0000000
FOXM1 0.0181099 -2.890122 0.000 0.040 1.0000000
PDGFB 0.0181099 -2.890122 0.000 0.040 1.0000000
PLOD2 0.0181099 -2.890122 0.000 0.040 1.0000000
BRAF 0.0181198 -1.890122 0.022 0.093 1.0000000
RAF1 0.0186879 -1.797013 0.036 0.120 1.0000000
TEAD1 0.0191611 -1.627088 0.029 0.107 1.0000000
STAT6 0.0206530 -1.160211 0.201 0.320 1.0000000
ITGAX 0.0240106 -1.077749 0.201 0.333 1.0000000
SFRP2 0.0259585 1.633440 0.137 0.040 1.0000000
DNMT3A 0.0334397 -2.475085 0.007 0.053 1.0000000
ITK 0.0334397 -2.475085 0.007 0.053 1.0000000
TGFBR3 0.0334397 -2.475085 0.007 0.053 1.0000000
IDH1 0.0338170 -2.212051 0.007 0.053 1.0000000
TAP2 0.0343940 -1.590562 0.043 0.120 1.0000000
ICAM3 0.0349601 2.569309 0.058 0.000 1.0000000
CX3CR1 0.0349781 2.279803 0.058 0.000 1.0000000
PTK2 0.0357934 -1.890122 0.036 0.107 1.0000000
ITGB1 0.0410603 -2.060047 0.022 0.080 1.0000000
ITGA5 0.0411131 -1.890122 0.014 0.067 1.0000000
TGFBR1 0.0420441 -1.890122 0.022 0.080 1.0000000
HAVCR2 0.0421759 -1.568194 0.029 0.093 1.0000000
PDCD1LG2 0.0462178 -1.720197 0.058 0.133 1.0000000
CXCR4 0.0491341 2.810317 0.050 0.000 1.0000000

4.7 T cell

X p_val avg_log2FC pct.1 pct.2 p_val_adj
LMNA 0.0000000 -2.500421 0.144 0.596 0.0000000
LYZ 0.0000000 5.012224 0.370 0.026 0.0000000
S100A9 0.0000000 -2.927510 0.020 0.141 0.0000000
MZB1 0.0000001 5.186095 0.171 0.006 0.0000415
ITGA4 0.0000034 -2.177944 0.023 0.096 0.0017019
AKT3 0.0000077 -2.010749 0.034 0.115 0.0038666
TP63 0.0000104 -3.338936 0.003 0.038 0.0051905
POU2AF1 0.0000151 4.105043 0.121 0.006 0.0075558
CTNNB1 0.0000233 -1.432046 0.099 0.212 0.0116370
CLCA1 0.0000506 -3.017008 0.004 0.038 0.0253111
KLF2 0.0000542 1.335583 0.245 0.096 0.0271111
ICOS 0.0000620 -2.531581 0.009 0.051 0.0309908
ITGB1 0.0000815 -1.456293 0.055 0.141 0.0407340
CIITA 0.0000910 1.757925 0.146 0.032 0.0455000
VWF 0.0002445 -2.156072 0.033 0.096 0.1222577
BST2 0.0002721 1.548146 0.172 0.058 0.1360731
SNAI2 0.0003326 -2.394078 0.011 0.051 0.1662792
COL5A1 0.0003460 -1.401701 0.126 0.224 0.1729756
CD79A 0.0003556 3.275774 0.089 0.006 0.1777809
VEGFB 0.0004002 2.911362 0.088 0.006 0.2001053
MCM6 0.0004793 -1.531581 0.042 0.109 0.2396466
LAMB3 0.0005225 -3.209653 0.004 0.032 0.2612385
EPHB4 0.0005691 -1.605582 0.039 0.103 0.2845465
CD177 0.0006646 -3.853509 0.001 0.019 0.3323038
CCL1 0.0006731 -4.116544 0.000 0.013 0.3365283
NFKB1 0.0009752 -1.747310 0.033 0.090 0.4876054
ELANE 0.0014990 -3.116544 0.003 0.026 0.7495067
FGFBP2 0.0015148 -2.853509 0.003 0.026 0.7574114
CD28 0.0015264 -1.209653 0.068 0.141 0.7632131
WNT5A 0.0015939 -2.531581 0.006 0.032 0.7969546
SMARCA4 0.0021909 -1.647059 0.024 0.071 1.0000000
STAT4 0.0022715 -1.233901 0.061 0.128 1.0000000
NFE2L2 0.0023851 -1.669085 0.021 0.064 1.0000000
CDK2 0.0024010 -1.309189 0.040 0.096 1.0000000
YAP1 0.0024948 -1.464467 0.044 0.103 1.0000000
MUC4 0.0030525 -1.268547 0.037 0.090 1.0000000
IL23A 0.0034345 -2.406051 0.012 0.045 1.0000000
BRCA1 0.0042586 -2.946619 0.002 0.019 1.0000000
ASCL2 0.0047895 -2.531581 0.004 0.026 1.0000000
PRF1 0.0048753 -1.332273 0.065 0.128 1.0000000
PLA2G2A 0.0052620 1.818916 0.072 0.013 1.0000000
TNC 0.0064767 -1.353244 0.044 0.096 1.0000000
THBD 0.0072925 -1.577385 0.024 0.064 1.0000000
APC 0.0077502 -1.347157 0.024 0.064 1.0000000
TGFBR1 0.0095454 -1.531581 0.018 0.051 1.0000000
KRAS 0.0097278 -1.894151 0.014 0.045 1.0000000
IL2RA 0.0098266 -1.268547 0.018 0.051 1.0000000
TCF7L2 0.0100215 -1.055143 0.064 0.122 1.0000000
PRKCA 0.0111701 -1.053534 0.038 0.083 1.0000000
CSF3 0.0111819 -1.531581 0.030 0.071 1.0000000
ERBB2 0.0124888 -1.329948 0.022 0.058 1.0000000
SELPLG 0.0128314 1.200222 0.092 0.032 1.0000000
GPX3 0.0128412 1.351062 0.092 0.032 1.0000000
CCL4 0.0134036 1.905824 0.139 0.071 1.0000000
TEAD4 0.0144091 -3.116544 0.003 0.019 1.0000000
TSC2 0.0145403 -2.853509 0.003 0.019 1.0000000
INSR 0.0151294 2.112275 0.060 0.013 1.0000000
SRC 0.0159590 -1.657112 0.023 0.058 1.0000000
ATR 0.0160740 -1.753974 0.012 0.038 1.0000000
ZEB1 0.0204785 -1.209653 0.032 0.071 1.0000000
FCGR3A 0.0228129 -3.309189 0.007 0.026 1.0000000
DERL3 0.0232827 2.351062 0.044 0.006 1.0000000
FOXP3 0.0234492 1.638344 0.055 0.013 1.0000000
FCRL5 0.0287359 1.991981 0.042 0.006 1.0000000
PTPRC 0.0294578 -1.406051 0.025 0.058 1.0000000
GZMB 0.0319442 -1.159613 0.039 0.077 1.0000000
MAP2K1 0.0319787 -1.379578 0.018 0.045 1.0000000
CD3G 0.0324317 -1.084122 0.030 0.064 1.0000000
CD14 0.0353312 1.991981 0.040 0.006 1.0000000
CLEC14A 0.0354823 2.223306 0.028 0.000 1.0000000
RB1 0.0354864 -2.209653 0.004 0.019 1.0000000
CLEC4C 0.0357515 -1.724227 0.004 0.019 1.0000000
ITGA1 0.0357515 -1.946619 0.004 0.019 1.0000000
NF1 0.0364439 -1.072150 0.059 0.103 1.0000000
AXIN2 0.0377469 -1.057650 0.022 0.051 1.0000000
CLDN5 0.0387038 -1.236125 0.027 0.058 1.0000000
MS4A1 0.0422443 -1.853509 0.008 0.026 1.0000000
CASP8 0.0465681 -2.531581 0.002 0.013 1.0000000
CCR3 0.0465681 -2.531581 0.002 0.013 1.0000000
CD68 0.0465681 -2.531581 0.002 0.013 1.0000000
CD86 0.0465681 -2.531581 0.002 0.013 1.0000000
CEACAM8 0.0465681 -2.531581 0.002 0.013 1.0000000
IL4 0.0465681 -2.531581 0.002 0.013 1.0000000
KITLG 0.0465681 -2.531581 0.002 0.013 1.0000000
MMP12 0.0465681 -2.531581 0.002 0.013 1.0000000
WNT3 0.0465681 -2.531581 0.002 0.013 1.0000000

4.8 Inflammatory fibroblast

X p_val avg_log2FC pct.1 pct.2 p_val_adj
LYZ 0.0000000 6.287856 0.316 0.007 0.0000000
SOCS3 0.0000000 -1.419312 0.344 0.612 0.0000000
MYC 0.0000000 -1.294029 0.242 0.454 0.0000000
NRP1 0.0000000 -1.423821 0.150 0.334 0.0000000
TGFBR3 0.0000000 -1.455502 0.098 0.239 0.0000000
NCAM1 0.0000000 -1.551870 0.070 0.191 0.0000000
CDKN1A 0.0000000 -1.170179 0.150 0.294 0.0000000
S100A9 0.0000000 -3.739739 0.005 0.056 0.0000000
ITGA5 0.0000000 -1.327045 0.083 0.178 0.0000000
MZB1 0.0000000 4.048226 0.056 0.004 0.0000000
IL6 0.0000000 -1.550195 0.053 0.129 0.0000000
CTNNB1 0.0000000 -1.056207 0.091 0.175 0.0000000
IFNGR2 0.0000000 -1.123829 0.069 0.143 0.0000000
COL6A3 0.0000000 -2.086878 0.014 0.056 0.0000000
XBP1 0.0000000 1.530351 0.107 0.043 0.0000000
ELN 0.0000000 -1.186266 0.057 0.115 0.0000000
MAFB 0.0000000 -1.297345 0.050 0.105 0.0000000
CDK2 0.0000000 -1.289077 0.040 0.091 0.0000000
CAV1 0.0000000 -1.573246 0.021 0.061 0.0000000
WNT5A 0.0000000 -1.725974 0.018 0.056 0.0000000
ZEB1 0.0000000 -1.243536 0.041 0.091 0.0000000
PREX2 0.0000000 -1.341989 0.028 0.068 0.0000000
SNAI2 0.0000000 -1.260591 0.035 0.078 0.0000000
ITGB1 0.0000000 -1.038400 0.051 0.098 0.0000000
IL6R 0.0000000 -1.098896 0.050 0.096 0.0000000
IFNGR1 0.0000000 -1.679670 0.013 0.040 0.0000000
MCM6 0.0000000 -1.165350 0.031 0.065 0.0000000
RET 0.0000000 -2.615806 0.004 0.022 0.0000000
MSH6 0.0000000 -1.419839 0.018 0.045 0.0000000
AXIN2 0.0000000 -1.080312 0.032 0.064 0.0000000
CD79A 0.0000000 2.745918 0.020 0.003 0.0000000
TWIST1 0.0000000 -1.082626 0.029 0.059 0.0000000
TGFBR1 0.0000000 -1.438957 0.015 0.037 0.0000000
TSC1 0.0000000 -1.110932 0.028 0.057 0.0000000
CCL2 0.0000000 -1.397968 0.020 0.044 0.0000000
POU2AF1 0.0000000 1.736458 0.031 0.010 0.0000000
CLCA1 0.0000000 -1.102431 0.022 0.046 0.0000000
APC 0.0000000 -1.082822 0.020 0.042 0.0000000
HLA-DRB1 0.0000000 1.202441 0.036 0.014 0.0000000
MSH3 0.0000000 -1.132460 0.021 0.043 0.0000000
MET 0.0000000 -1.393288 0.012 0.031 0.0000000
ATR 0.0000000 -1.103189 0.020 0.042 0.0000000
FGF2 0.0000000 -1.192647 0.016 0.036 0.0000000
SERPINE1 0.0000000 1.048027 0.114 0.079 0.0000000
CD79B 0.0000000 -1.235554 0.018 0.036 0.0000003
TBK1 0.0000000 -1.511470 0.006 0.017 0.0000042
SNAI1 0.0000000 -1.496363 0.007 0.018 0.0000060
BRCA1 0.0000007 -1.407133 0.006 0.015 0.0003290
CLDN5 0.0000031 -1.096432 0.015 0.027 0.0015597
ROR1 0.0000058 -1.011543 0.010 0.020 0.0028850
CD27 0.0000170 1.617814 0.010 0.003 0.0085049
C1QC 0.0000378 1.163691 0.013 0.006 0.0188797
PIK3CG 0.0000539 1.121992 0.016 0.008 0.0269355
KITLG 0.0000712 -1.299965 0.005 0.011 0.0355818
DERL3 0.0001016 1.163691 0.013 0.006 0.0508171
MUC4 0.0001590 -1.012664 0.009 0.017 0.0795059
KRAS 0.0002869 -1.073348 0.006 0.012 0.1434569
CD160 0.0004277 -1.022431 0.006 0.011 0.2138476

4.9 Myofibroblast

X p_val avg_log2FC pct.1 pct.2 p_val_adj
LYZ 0.0000000 5.702643 0.304 0.009 0.0000000
ATF3 0.0000000 -1.328048 0.276 0.521 0.0000000
ITGB1 0.0000000 -1.404628 0.137 0.321 0.0000000
S100A9 0.0000000 -4.387998 0.004 0.073 0.0000000
GPX3 0.0000000 -1.237800 0.141 0.275 0.0000000
ANGPT1 0.0000000 -1.220189 0.074 0.163 0.0000001
MCM6 0.0000001 -2.187759 0.008 0.044 0.0000696
ANGPT2 0.0000002 -1.094796 0.060 0.125 0.0000963
HGF 0.0000003 -1.312879 0.032 0.084 0.0001304
IFNGR2 0.0000005 -1.143842 0.054 0.115 0.0002280
MSH6 0.0000013 -1.718274 0.019 0.059 0.0006592
STAT4 0.0000034 -1.321347 0.036 0.084 0.0017087
XBP1 0.0000057 1.371909 0.078 0.032 0.0028300
STING1 0.0000081 -1.015160 0.045 0.095 0.0040614
APC 0.0000157 -1.363446 0.024 0.062 0.0078260
DNMT3A 0.0000183 -1.477266 0.021 0.056 0.0091613
IFNGR1 0.0000236 -2.799194 0.003 0.023 0.0117755
ZEB1 0.0000255 -1.120572 0.036 0.078 0.0127292
ITGA1 0.0000675 -1.331187 0.023 0.057 0.0337614
ELN 0.0005893 1.155003 0.046 0.019 0.2946263
MSH3 0.0006019 -1.691390 0.007 0.026 0.3009656
TWIST1 0.0009254 -1.216738 0.020 0.045 0.4627068
IFNG 0.0011200 -2.855777 0.001 0.012 0.5599882
ATR 0.0011950 -1.299727 0.016 0.039 0.5975033
WNT3A 0.0024269 -1.025277 0.025 0.050 1.0000000
LAMB3 0.0025390 -1.450793 0.009 0.026 1.0000000
TGFBR3 0.0027791 -1.007780 0.032 0.058 1.0000000
KITLG 0.0039232 -1.503261 0.009 0.025 1.0000000
FZD7 0.0057511 -1.091207 0.020 0.040 1.0000000
CCL17 0.0058385 1.368224 0.020 0.006 1.0000000
RET 0.0078475 -1.418372 0.008 0.022 1.0000000
CCL5 0.0081746 2.166591 0.012 0.002 1.0000000
C1QC 0.0089212 2.014588 0.014 0.003 1.0000000
TBK1 0.0126526 -1.740300 0.005 0.015 1.0000000
PLA2G2A 0.0137785 1.529161 0.027 0.012 1.0000000
MZB1 0.0172064 1.488519 0.019 0.007 1.0000000
TGFBR1 0.0181777 -1.013319 0.014 0.028 1.0000000
VCAM1 0.0217557 -1.155337 0.009 0.021 1.0000000
PPARGC1A 0.0322311 -1.219468 0.009 0.020 1.0000000
PDGFC 0.0335545 1.545102 0.011 0.003 1.0000000
PDGFRA 0.0421733 -1.292841 0.008 0.018 1.0000000

4.10 Tumor-like fibroblast

X p_val avg_log2FC pct.1 pct.2 p_val_adj
LYZ 0.0000000 5.669945 0.325 0.006 0.0000000
S100A9 0.0000000 -4.821908 0.004 0.142 0.0000005
EGFR 0.0000114 -2.291393 0.036 0.155 0.0056833
SOCS3 0.0000500 1.139323 0.394 0.219 0.0249898
MLH1 0.0002148 -1.473984 0.066 0.181 0.1073955
BMI1 0.0002221 -2.937385 0.007 0.071 0.1110503
CIITA 0.0007241 1.859916 0.172 0.058 0.3620561
CEACAM1 0.0076750 -3.406870 0.000 0.026 1.0000000
GZMH 0.0076754 -3.143836 0.000 0.026 1.0000000
ROR1 0.0086109 -2.406870 0.007 0.045 1.0000000
PGF 0.0104780 -2.143836 0.011 0.052 1.0000000
CLEC14A 0.0113113 -1.143836 0.058 0.129 1.0000000
AKT3 0.0115461 -1.558873 0.029 0.084 1.0000000
MYC 0.0143852 -1.153114 0.080 0.155 1.0000000
FGFR3 0.0155623 -2.406870 0.004 0.032 1.0000000
HIF1A 0.0207630 -1.449939 0.033 0.084 1.0000000
ITGA4 0.0211415 -2.821908 0.000 0.019 1.0000000
TNFSF10 0.0211415 -2.821908 0.000 0.019 1.0000000
APC 0.0239064 -1.200419 0.029 0.077 1.0000000
IGF1 0.0254134 -1.821908 0.015 0.052 1.0000000
CD5 0.0320991 2.500020 0.029 0.000 1.0000000
CAV1 0.0330054 -1.184478 0.040 0.090 1.0000000
PLA2G2A 0.0332789 2.036073 0.055 0.013 1.0000000
CD79A 0.0452741 2.178092 0.026 0.000 1.0000000
AXIN2 0.0494633 -1.214225 0.044 0.090 1.0000000

4.11 Vessel-associated fibroblast

X p_val avg_log2FC pct.1 pct.2 p_val_adj
PDK4 0.0000000 -2.068946 0.415 0.819 0.0000000
VEGFA 0.0000000 -1.266291 0.666 0.915 0.0000000
LYZ 0.0000000 5.418567 0.297 0.012 0.0000000
CDKN1A 0.0000000 1.751711 0.638 0.252 0.0000000
FOS 0.0000000 -1.001443 0.761 0.932 0.0000000
SH2D1B 0.0000000 -3.017663 0.042 0.260 0.0000000
DUSP1 0.0000000 1.186252 0.639 0.415 0.0000000
BCL2L1 0.0000000 1.353766 0.410 0.187 0.0000000
CSF3 0.0000000 -1.842843 0.050 0.170 0.0000000
ELN 0.0000000 1.267258 0.167 0.075 0.0000000
BMP1 0.0000000 1.094448 0.149 0.072 0.0000000
SNAI2 0.0000000 2.553879 0.053 0.011 0.0000000
FZD7 0.0000000 -1.530513 0.044 0.113 0.0000000
TGFB1 0.0000000 1.853440 0.070 0.020 0.0000000
ATF3 0.0000000 1.399369 0.097 0.040 0.0000000
LDHA 0.0000000 -1.279256 0.053 0.116 0.0000000
DERL3 0.0000000 2.167988 0.052 0.016 0.0000000
COL1A1 0.0000000 1.040838 0.109 0.054 0.0000000
PLVAP 0.0000000 1.056990 0.086 0.040 0.0000000
PDGFRB 0.0000000 1.231951 0.064 0.027 0.0000005
PDPN 0.0000000 1.143091 0.079 0.038 0.0000007
SERPINE1 0.0000000 1.131188 0.039 0.012 0.0000010
COL4A1 0.0000000 1.179814 0.059 0.026 0.0000072
VSIR 0.0000000 -1.835687 0.013 0.042 0.0000090
BCL2 0.0000000 -1.225521 0.034 0.073 0.0000120
HLA-B 0.0000000 1.188230 0.052 0.022 0.0000172
HLA-DRA 0.0000000 1.433585 0.045 0.018 0.0000191
PLA2G2A 0.0000001 1.051379 0.057 0.026 0.0000696
MUC4 0.0000002 -1.154818 0.035 0.071 0.0001012
IFNGR1 0.0000003 -1.370172 0.020 0.050 0.0001446
ADAMTS4 0.0000004 1.604505 0.026 0.007 0.0001816
CLDN5 0.0000025 1.065041 0.069 0.038 0.0012465
STING1 0.0000025 1.231951 0.036 0.015 0.0012717
NRP1 0.0000037 -1.630545 0.017 0.041 0.0018505
RB1 0.0000064 -2.201008 0.004 0.019 0.0032086
CHEK2 0.0000066 1.982723 0.018 0.004 0.0032977
IL23A 0.0000177 -1.337414 0.016 0.038 0.0088600
CA7 0.0000436 -1.291146 0.014 0.033 0.0218208
MMP2 0.0000437 1.591354 0.019 0.006 0.0218323
CTSG 0.0000642 1.073254 0.022 0.008 0.0320869
SOX9 0.0000646 1.696837 0.023 0.008 0.0323022
EGF 0.0001074 -1.699877 0.006 0.020 0.0537042
CTSW 0.0001287 1.270086 0.024 0.010 0.0643623
CD274 0.0001908 -1.194582 0.013 0.030 0.0954242
C1QC 0.0002158 1.660795 0.014 0.004 0.1079068
ERBB3 0.0003021 1.267575 0.021 0.008 0.1510675
HLA-DPB1 0.0004895 1.231951 0.020 0.008 0.2447286
CD5 0.0005308 1.123245 0.024 0.011 0.2654235
CSF1R 0.0010227 1.338151 0.016 0.006 0.5113434
CCR4 0.0018563 1.048644 0.016 0.007 0.9281325
PLK1 0.0021844 -1.031083 0.014 0.027 1.0000000
CYBB 0.0027872 1.631882 0.010 0.003 1.0000000
CLEC14A 0.0029999 1.187752 0.020 0.010 1.0000000
MRC1 0.0031231 1.553879 0.010 0.003 1.0000000
SRC 0.0039141 1.497296 0.012 0.004 1.0000000
SELPLG 0.0044567 1.254319 0.013 0.005 1.0000000
CCL5 0.0072534 1.197736 0.013 0.005 1.0000000
HGF 0.0073406 1.221304 0.013 0.006 1.0000000
HAVCR2 0.0074647 1.068453 0.016 0.007 1.0000000
TGM2 0.0086653 -1.005548 0.010 0.019 1.0000000
TNFSF4 0.0086985 -1.545656 0.003 0.010 1.0000000
EPHA4 0.0108605 -1.002514 0.009 0.018 1.0000000
PLOD2 0.0175196 -1.253475 0.004 0.010 1.0000000
CCL7 0.0183386 1.138842 0.011 0.005 1.0000000

4.12 inflame

X p_val avg_log2FC pct.1 pct.2 p_val_adj
ACTA2 0.0000000 3.958411 0.831 0.118 0.0000000
FGFR1 0.0000000 4.891728 0.668 0.039 0.0000000
IRS1 0.0000000 4.260923 0.353 0.021 0.0000000
LAMB3 0.0000000 3.550631 0.448 0.048 0.0000000
EGR1 0.0000000 3.266214 0.730 0.232 0.0000000
MYH11 0.0000000 3.899491 0.320 0.024 0.0000000
COL4A1 0.0000000 3.602405 0.325 0.030 0.0000000
SOCS3 0.0000000 3.709789 0.297 0.041 0.0000000
PDGFB 0.0000000 3.978149 0.206 0.016 0.0000000
LYZ 0.0000000 -1.470664 0.876 0.963 0.0000000
XBP1 0.0000000 -1.846656 0.425 0.821 0.0000000
COL5A1 0.0000000 3.584808 0.199 0.018 0.0000000
SRC 0.0000000 3.107971 0.250 0.033 0.0000000
CSF1 0.0000000 2.768905 0.321 0.058 0.0000000
TP63 0.0000000 4.180445 0.155 0.009 0.0000000
LRP1 0.0000000 2.105701 0.334 0.080 0.0000000
RORC 0.0000000 -2.439948 0.149 0.564 0.0000000
TGFBR3 0.0000000 2.541883 0.242 0.047 0.0000000
SMOC2 0.0000000 3.284565 0.115 0.012 0.0000000
INSR 0.0000000 -1.711842 0.208 0.553 0.0000000
FOS 0.0000000 1.443122 0.616 0.354 0.0000000
AMOTL2 0.0000000 1.801609 0.256 0.080 0.0000000
LAMC2 0.0000000 3.237028 0.085 0.010 0.0000000
JUNB 0.0000000 1.446829 0.412 0.189 0.0000000
LGR6 0.0000000 3.368110 0.073 0.007 0.0000000
CAV1 0.0000000 4.038824 0.057 0.004 0.0000000
BCL2 0.0000000 2.925022 0.089 0.012 0.0000000
SNAI2 0.0000000 2.395224 0.130 0.029 0.0000000
VEGFA 0.0000000 -1.838260 0.128 0.367 0.0000000
FGF1 0.0000000 2.575438 0.089 0.016 0.0000000
AKT3 0.0000000 3.308839 0.050 0.005 0.0000000
EPHA2 0.0000000 -1.957226 0.091 0.292 0.0000000
ERBB3 0.0000000 -2.330905 0.048 0.227 0.0000000
CCL28 0.0000000 -2.301334 0.044 0.212 0.0000000
GATA3 0.0000000 -2.327674 0.050 0.214 0.0000000
COL11A1 0.0000000 3.473226 0.034 0.003 0.0000000
CD248 0.0000000 2.679230 0.052 0.008 0.0000000
ELN 0.0000000 1.778255 0.103 0.030 0.0000000
EGFR 0.0000000 1.070965 0.263 0.136 0.0000000
FZD7 0.0000000 1.307314 0.163 0.068 0.0000000
WNT3A 0.0000000 2.206440 0.066 0.015 0.0000000
PGF 0.0000000 2.681813 0.043 0.007 0.0000000
BCL2L1 0.0000000 -1.169375 0.183 0.330 0.0000000
ELANE 0.0000000 2.875664 0.032 0.004 0.0000000
TGFB1 0.0000000 1.878280 0.059 0.016 0.0000000
STING1 0.0000000 2.051763 0.048 0.012 0.0000000
TGFBR2 0.0000000 1.040376 0.188 0.100 0.0000000
ICAM1 0.0000000 1.725992 0.053 0.016 0.0000006
SOD2 0.0000000 -1.038526 0.133 0.245 0.0000009
PTGS2 0.0000000 2.507442 0.027 0.005 0.0000019
NRP1 0.0000000 1.484542 0.066 0.025 0.0000146
MYC 0.0000000 1.140729 0.144 0.077 0.0000192
EPHA4 0.0000001 2.194367 0.028 0.006 0.0000416
TAP2 0.0000001 1.157530 0.094 0.043 0.0000440
BMP1 0.0000001 1.057116 0.107 0.052 0.0000626
FGF2 0.0000003 2.459420 0.021 0.004 0.0001269
TEAD4 0.0000003 2.566336 0.020 0.003 0.0001414
ITGA5 0.0000003 1.829370 0.039 0.012 0.0001438
CXCL5 0.0000004 -2.010590 0.025 0.086 0.0001777
FBLN1 0.0000004 2.258213 0.023 0.005 0.0002037
IKZF2 0.0000005 -1.903984 0.020 0.077 0.0002579
MMRN1 0.0000017 -1.773971 0.021 0.076 0.0008366
CDH5 0.0000027 2.058189 0.025 0.006 0.0013468
DERL3 0.0000057 -2.134104 0.011 0.055 0.0028134
CD14 0.0000105 -1.674342 0.023 0.072 0.0051208
TNFRSF13C 0.0000140 -1.582056 0.025 0.074 0.0068718
GNLY 0.0000287 1.944847 0.021 0.006 0.0140567
AURKB 0.0000692 1.749200 0.021 0.006 0.0339260
PDK4 0.0000726 -1.032869 0.044 0.095 0.0355545
IGF1 0.0001312 1.566336 0.030 0.011 0.0642860
NF1 0.0001416 -1.001948 0.048 0.097 0.0694066
MKI67 0.0001536 1.642285 0.021 0.006 0.0752780
S100A9 0.0001549 -1.609514 0.030 0.072 0.0759233
SLC13A3 0.0002328 -1.312499 0.025 0.064 0.1140755
ITGA1 0.0002758 2.499221 0.011 0.002 0.1351235
CCR7 0.0002767 2.151298 0.014 0.003 0.1355994
IL6R 0.0004934 1.473226 0.025 0.009 0.2417702
ICAM3 0.0008453 -1.153556 0.028 0.064 0.4141810
TWIST1 0.0008925 1.752749 0.018 0.006 0.4373128
PLOD2 0.0011845 -1.073075 0.018 0.048 0.5803812
CD2 0.0012053 2.063835 0.012 0.003 0.5906017
PDCD1LG2 0.0012053 2.063835 0.012 0.003 0.5906017
TBX21 0.0013196 -1.010590 0.034 0.069 0.6465992
CIITA 0.0013932 -1.587470 0.016 0.044 0.6826864
ATF3 0.0016477 -1.226088 0.053 0.092 0.8073496
CCL2 0.0019279 1.981373 0.012 0.003 0.9446911
ENG 0.0024150 1.268655 0.027 0.011 1.0000000
CEACAM1 0.0025487 -1.517080 0.011 0.034 1.0000000
MAFB 0.0026463 -1.871070 0.005 0.026 1.0000000
TNFRSF9 0.0028628 -1.009166 0.028 0.059 1.0000000
FOSL1 0.0034988 -1.114046 0.021 0.048 1.0000000
ZEB1 0.0040517 1.414333 0.020 0.008 1.0000000
FGFR3 0.0044443 -3.134104 0.000 0.014 1.0000000
CD4 0.0054059 1.519030 0.016 0.006 1.0000000
IFITM1 0.0054059 1.519030 0.016 0.006 1.0000000
SMAD2 0.0069379 1.200208 0.025 0.011 1.0000000
KIT 0.0069600 -1.767565 0.005 0.022 1.0000000
IL2RB 0.0070795 1.519030 0.016 0.006 1.0000000
FLT1 0.0071928 1.151298 0.027 0.013 1.0000000
CDCA7 0.0082552 1.175546 0.025 0.012 1.0000000
PDGFA 0.0082552 1.175546 0.025 0.012 1.0000000
HAVCR2 0.0133219 -1.096629 0.009 0.026 1.0000000
CXCL12 0.0134173 1.325328 0.018 0.008 1.0000000
NRAS 0.0175183 1.212699 0.020 0.009 1.0000000
CCR6 0.0376074 -1.308133 0.005 0.017 1.0000000
E2F1 0.0455045 -1.202339 0.014 0.029 1.0000000
MUC2 0.0498289 -2.282403 0.011 0.023 1.0000000

5. Supplements

For original pictures and more details, please use the google drive link: ENT MERFISH Supplement